GWAS, eigenvec in R
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3.7 years ago
whateverer • 0

Hi All,

I know that a lot of people asked about plink PCA and eigenvec, but i am a basic learner and have a difficulty understanding what they mean exactly.. Hope there is an angel to HELP me!

I have done plink PCA and am trying to make a graph in R by eigenvec file

raw-GWA-data.hapmap3r2.pruned.eigenvec

1 1 2 0.00675506 -0.00102713 0.000255009 0.00506672 0.00518335 2 2 1 0.00787777 -0.000930726 -0.00106701 -0.000330665 0.00495431 3 3 2 0.00746506 -0.00135015 0.00066044 -0.00368828 -0.00336739 4 4 2 0.00790253 -0.000707524 0.00284133 -0.00700586 0.000281037 5 5 2 0.00755939 -0.000803938 0.000926113 -0.000723133 0.00029433 6 6 2 0.00773069 -0.000876533 -0.00459124 -0.00200765 -0.001773 7 7 2 0.00795287 -0.00143945 -0.00331132 -0.00125819 -0.00366881 8 8 2 0.00761576 -0.00143091 0.00179961 0.00132296 0.0060271 9 9 2 0.00773385 -0.000960629 6.92423E-05 0.00292627 -0.000748113 10 10 2 0.00753494 -0.00101162 0.000936778 0.00199789 -0.000327348 ... 2395

and this is the script that i wrote

data=read.table("raw-GWA-data.hapmap3r2.pruned.eigenvec",h=F,skip=1) cont=which(data$V3=="1") case=which(data$V3=="2") CEU=which(data$V3=="3") CHB=which(data$V3=="4") JPT=which(data$V3=="5") YRI=which(data$V3=="6") pdf("pca-ancestry-plot.pdf") plot(0,0,pch="",xlim=c(-0.1,0.05),ylim=c(-0.05,0.1),xlab="principal component 1", ylab="principal component 2") points(data$V4[JPT],data$V5[JPT],pch=20,col="PURPLE") points(data$V4[CHB],data$V5[CHB],pch=20,col="PURPLE") points(data$V4[YRI],data$V5[YRI],pch=20,col="GREEN") points(data$V4[CEU],data$V5[CEU],pch=20,col="RED") par(cex=0.5) points(data$V4[cont],data$V5[cont],pch="+",col="BLACK") points(data$V4[case],data$V5[case],pch="+",col="BLACK") abline(h=0.072,col="gray32",lty=2) dev.off() quit() n

After this, I got a pdf file. It doesn't show the points though; only have x,y axises/names(principal components)

How could i get the right result....?

Thank you.

eigenvec GWAS R program • 1.1k views